Resurrected Proteins and the Case for Biological Evolution

resurrectedproteinsandthecase

BY FAZALE RANA – OCTOBER 14, 2013

Recently, a team of researchers from Spain resurrected a 4-billion-year-old version of a protein that belongs to a class of proteins known as thioredoxins. The ability to resurrect ancient proteins using principles integral to the evolutionary paradigm is the type of advance that many scientists point to as evidence for biological evolution. In this article, I discuss how this work can be seamlessly accommodated within a creation/design paradigm.

Recently, a team of biochemists from Spain resurrected an ancient version of a protein, known as a thioredoxin. The successful restoration of this antiquated protein is the kind of advance that many scientists point to as evidence for the evolutionary paradigm.

Presumably, the protein they “brought back to life” would have been as it was 4 billion years ago.1 By studying the structure and function of the ancient thioredoxin, the research team was able to gain insight into the biology of some of the first life-forms on Earth. This is not the first time biochemists have pulled off this feat. Over the last several years, life scientists have announced the re-creation of a number of ancient proteins.2

The procedure for resurrecting ancient proteins makes use of evolutionary trees that are built using the amino acid sequences of extant proteins. From these trees, scientists infer the structure of the ancestral protein. They then go into the lab and make that protein—and more often than not, the molecule adopts a stable structure with discernible function. It is remarkable to think that scientists can use evolutionary trees to interpolate the probable structure of an ancestral protein to then make a biomolecule that displays function. I truly understand why people would point to this type of work as evidence for biological evolution.

So, how does someone who advocates for intelligent design/creationism make sense of scientists’ ability to resurrect ancient proteins?

For the sake of brevity, I will provide a quick response to this question. For a more detailed discussion of the production of ancient thioredoxins and how I view resurrected proteins from a design/creation model perspective listen to the August 12, 2013 episode of Science News Flash.

To appreciate a design/creation interpretation of this work, it is important to first understand how scientists determine the amino acid sequence for ancient proteins. Evolutionary biologists make an inference by comparing amino acid sequences of extant proteins. (In this most recent study, scientists compared around 200 thioredoxins from organisms representing all three domains of life.) Based on the patterns of similarities and differences in the sequences, they propose evolutionary relationships among the proteins.

The assumption is that the differences in the amino acid sequences of extant proteins stem from mutations to the genes encoding the proteins. Accordingly, these mutations would be passed on to subsequent generations. As the different lineages diverge, different types of mutations would accrue in the protein-coding genes in the distinct lineages. The branch points, or nodes, in the evolutionary tree, would then represent the ancestral protein shared by all proteins found in the lineages that split from that point. Researchers then infer the most likely amino acid sequence of the ancestral protein by working their way backwards from extant amino acid sequences of proteins which fall along the branches that stem from the node.

At this juncture, it is important to note that evolutionary biologists actively choose to interpret the similarities and differences in the amino acid sequences of extant proteins from an evolutionary perspective. I maintain that it is equally valid to interpret the sequence similarities and differences from a design/creation standpoint as well. With this approach, the archetype takes the place of the common ancestor. And the differences in the amino acid sequences represent variations around an archetypical design shared by all the proteins that are members of a particular family, such as the thioredoxins. In light of this concept, it is interesting the researchers discovered that the structure of ancient thioredoxins is highly conserved moving back through time, with only limited variation in the structure, which varied around a core design.

What about the process for determining the ancestral/archetypical sequence from an evolutionary tree? Doesn’t this fact run contrary to a design explanation?

Not necessarily. Consider the variety of automobiles that exist. These vehicles are all variants of an archetypical design. Even though automobiles are the products of intelligent agents, they can be organized into an “evolutionary tree” based on design similarities and differences. In this case, the nodes in the tree represent the core design of the automobiles that are found on the branches that arise from the node.

By analogy, one could also regard the extant members of a protein family as the work of a Designer. Just like automobiles, the protein variants can be organized into a tree-like diagram. In this case the nodes correspond to the common design elements of the proteins found on the branches.

In my view, when evolutionary biologists uncover what they believe to be the ancestral sequence of a protein family, they are really identifying

Endnotes

  1. Alvaro Ingles-Prieto et al., “Conservation of Protein Structure over Four Billion Years,” Structure21 (September 3, 2013): 1690–97.
  2. For example see Michael J. Harms and Joseph W. Thornton, “Analyzing Protein Structure and Function Using Ancestral Gene Reconstruction,” Current Opinion in Structural Biology 20 (June 2010): 360–66.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/todays-new-reason-to-believe/read/tnrtb/2013/10/15/resurrected-proteins-and-the-case-for-biological-evolution

A Good Reason for Evil

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What is evil? Could it have a purpose? Here is a view of evil from an adult rather than a childish perspective.

The first step in answering the problem of evil is this: We’ve got to get clear on what this thing “evil” actually is. It does seem to follow that if God created all things, and evil is a thing, then God created evil. This is a valid syllogism. If the premises are true, then the conclusion would be true as well.

The problem with that line of reasoning is that the second premise is not true. Evil is not a thing. The person who probably explained it best was St. Augustine, and then Thomas Aquinas picked up on his solution. Others since them have argued that evil has no ontological status in itself.

The word ontology deals with the nature of existence. When I say that evil has no ontological status, I mean that evil, as a thing in itself, does not exist.

Let me give you an illustration to make this more clear. We talk about things being cold or warm. But coldness is not a thing that exists in itself; it has no ontological status. Coldness is the absence of heat. When we remove heat energy from a system, we say it gets colder.

“Cold” isn’t a thing. It’s a way of describing the reduction of molecular activity resulting in the sensation of heat. So the more heat we pull out of a system, the colder it gets. Cold itself isn’t being “created.” Cold is a description of a circumstance in which heat is missing. Heat is energy which can be measured. When you remove heat, the temperature goes down. We call that condition “cold,” but there is no cold “stuff” that causes that condition.

Here’s another way of looking at it. Did you ever eat a donut hole? I don’t mean those little round sugar-coated lumps you buy at the donut shop. I mean the hole itself. Donut holes are actually what’s left when the middle is cut out of a donut. There’s a space called a hole, a “nothing,” the condition that exists when something is taken away. Same thing with a shadow. Shadows don’t exist as things in themselves; they’re just the absence of light.

Evil is like that. Evil isn’t like some black, gooey stuff floating around the universe that gloms onto people and causes them to do awful things. Evil is the absence of good, a privation of good, not a thing in itself.

When God created the universe, he created everything good. He made a universe that was perfectly good. Everything was as it should be. After God was completely done with creating everything, something happened that reduced the good in the world. That loss of good is called evil.

That’s why in Genesis 1 we read “it was good” many times. From the record we know that God didn’t create evil. But something did happen in which evil-the loss of good-took place, and as a result a lot of other grotesque things came about.

So donut holes don’t exist; they’re just the absence of donut. Shadows don’t exist; they’re just the absence of light. And evil doesn’t exist; it’s just the absence of good.

The next question is, if God created everything good, why would He allow evil to infect His creation?

Satan would be the first example of an independent source of evil. Adam and Eve would also be a source of evil with regard to the human race. They didn’t get Satan’s evil; they initiated their own. Satan influenced them–he made his own hole in goodness–but Adam and Eve made their own holes in goodness. They’re responsible for their own evil.

It isn’t that Satan did something bad and passed that stuff on to them, because evil is not a stuff. This is a key point in this discussion. They cannot “dip into” evil because it’s not a thing to dip into. When we make a shadow, we don’t do it with shadow stuff, but by blocking existing light.

In the same way, evil doesn’t cause our actions. In fact, it’s the other way around. Our actions are what cause evil-or the loss of goodness-in us, and that loss of goodness does have an impact on future actions, giving us a predisposition to cause further evil.

God did not create Adam and Eve with bad stuff in them. What He did was to create them with a capability to rebel against Him or choose to do wrong. This is called moral free will, and it’s a good thing, but it can be used for bad. It can be used to rebel against God, which digs out a hole in goodness, so to speak.

Satan and man both used their free moral agency to originate actions that fell short of the goodness of God. I’m sure God had a good reason for allowing evil. It has caused a lot of suffering, but that suffering has, in turn, also brought about a lot of good under God’s direction.

When you forgive someone who’s wronged you and you treat him kindly, is that a good thing? Sure it is, but you couldn’t forgive him if he hadn’t done something bad against you. I’m not saying that we should do evil so that the good of forgiveness could come about. I’m showing that it’s not a contradiction to claim that good can come out of evil.

It’s not good to promote evil itself, but one of the things about God is that He’s capable of taking a bad thing and making good come out of it. Mercy is one example of that. Without sin there would be no mercy. That’s true of a number of good things: bearing up under suffering, dealing with injustice, acts of heroism, forgiveness, long-suffering. These are all virtues that cannot be experienced in a world with no sin and evil.

Now the real question at this point is, “Was it worth it? Good can come out of evil, but was it worth it in the long run, the measure of good that comes out of the measure of evil in the world?” And my response is that the only One who could ever know that is God. You and I couldn’t know that because our perspective is too limited. Only God is in a position to accurately answer that question.

Apparently God thinks that, on balance, the good is going to outweigh the evil that caused the good, or else He wouldn’t have allowed it to happen. Christ paid a tremendous price, an example of the tremendous love God had for us. God would not be able to show His sacrificial love unless there was something to sacrifice for.

Here’s the problem, and this is why we don’t think that, on balance, it’s really a fair trade. We think that life is about giving us pleasure and making us happy. That’s what we think. This view is very prevalent in the United States. Our personal happiness, pleasure, and enjoyment are the most important things in life.

That’s not what the Bible teaches at all, though. There are aspects of enjoyment, but the ultimate reason we were created was not so we can have fun and enjoy life. God’s purpose for creating us was to develop us into certain types of people who were fit to spend eternity with Him. He does that by conforming us to His image by helping us grow through the process of living in a fallen world.

This is part of the message of the book of Hebrews. Even Jesus was conformed-made mature-by the process of suffering. In God’s mind, the goal of the process-being conformed to the image of His Son-is a much greater good than the bad of the evil that we have to put up with on this earth. The balance is definitely on the side of good.

I admit that this is not an easy issue, and part of the reason is that we bring some baggage to the discussion. Part of the baggage is that we have this idea that if God put us here on this earth and created the world for us to live in, then it seems to make sense that the summum bonum-the greatest good-is our immediate sense of personal pleasure and satisfaction. Therefore, if there is some circumstance in which we can’t have immediate satisfaction, then God must either have abandoned us, not exist, or be evil for allowing such a thing.

Last weekend I had a conversation with a young man about homosexuality. He challenged me with this point: Why would God create people as homosexuals if He didn’t want them to experience the pleasure of homosexual sex?

Now, of course, I didn’t agree with Him that God created people to be homosexuals. It wasn’t God’s design that they have this desire. But even if I conceded such a thing, why must I admit that-since one was created with a capacity for pleasure-only a mean, cruel God would allow conditions in which they’d have to say no to that pleasure?

When you think about it for a moment, doesn’t it strike you as odd that we’ve developed a view that in order for us to acknowledge God as good, He must give liberty to all of our passions? And if God doesn’t give liberty to all of our passions-if He doesn’t allow us what we want, when we want it-if He ever asks for self sacrifice, if He ever allows a condition in which we hurt, in which we suffer, in which we are inconvenienced, if He ever allows a circumstance in which our bodily desires are not given full reign, then certainly He must be a cruel God? Isn’t that an odd view?

Do you know what kind of person thinks that way? A child. A child sees what it wants and goes to get it, and if it’s stopped, that child puts up a fuss.

I was with a little two-year-old today who wanted to go into the house while wearing muddy shoes. She was stopped, and she put up a fuss when her shoes were removed. Mom and Dad knew, though, that there were other things more important than their daughter’s desires at that moment. Now she didn’t understand it. All she knew was what she wanted (understandably, by the way, she’s a two-year-old; that’s the way two-year-olds think).

Unfortunately, we’ve bred a society that are, in many ways, like a bunch of adult two-year-olds, grown-ups who believe it’s their divine right to feel every pleasure they can possibly feel, to never encounter any difficulty, any pain, any suffering. And if they do, then God must be a cruel God.

Now I realize that some of you might be thinking, Come on, Koukl, you’re really whitewashing this, aren’t you. How can so much egregious suffering be justified?

I don’t at all mean to brush away the terrible impact of evil on people’s lives. But I’m talking about a frame of mind that we do seem to have, a frame of mind that we are first and our pleasures are first and God owes that to us. And if He denies us our pleasures to any degree, then there must be something wrong with Him.

Now if God is a good God, and He denies us our pleasures, then I’ll tell you one thing, there’s a good reason He does so. That’s what it means to be a good God. I’m not going to buy the idea-the infantile idea that Americans have-that in order for God to be considered good, He has to give me everything I want, when I want it, or conversely, He must protect me from every injury and every difficulty. No, it’s fair to say that God has allowed suffering in the world for very good reasons, even though we’re not clear on all of those reasons.

By the way, what’s the alternative? If you conclude there’s no God because of the existence of evil, then there’s no possibility of ever redeeming that evil for good.

British philosopher Bertrand Russell said that no one can sit at the bedside of a dying child and still believe in God. My response to Mr. Russell is, “What would you say to a dying child?” What could an atheist say? “Too bad”? “Tough luck”? “Bum deal”? You see, in that circumstance, there’s no possibility of redemption for that evil. In fact, it doesn’t seem to make sense to even call it evil at all if there is no God.

But with God, at least there’s the possibility that the evil can be used for good. That’s the promise of the Scriptures.

And so, instead of the syllogism, “God created all things, and evil is a thing, therefore God created evil,” we start from a different point. “All things God created are good-which is what the text says-and evil isn’t good, therefore God didn’t create evil.” Then we can progress to, “If God created all things, and God didn’t create evil, then evil is not a thing.”

You see, those two syllogisms are just as valid as the first one (if God created all things, and evil is a thing, then God created evil), and it seems that the premises are more reliable. The premises seem to be accurate and true.

The questions we have to ask ourselves are: Do we have reason to think that God is good, and do we have reason to think that evil is not a thing? If we have good reasons to think those two things, then our new set of syllogisms work.

We can then strongly trust that when God does allow a privation of good (evil) to influence our lives, He does it not for evil designs, but ultimately for good purposes.


This is a transcript of a commentary from the radio show “Stand to Reason,” with Gregory Koukl. It is made available to you at no charge through the faithful giving of those who support Stand to Reason. Reproduction permitted for non-commercial use only. ©1997 Gregory Koukl

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The Origin of Evil

By Douglas L. Duncan, December 15, 2018

“The perplexing concept of evil eternally pleads the mind of God.”
– Douglas L. Duncan

If you have ever asked yourself any variation of the question, “Might there be a single source where the whole of evil came from, and if it is indeed a source at all, then what is it?”, both a belief in that which is unseen, coupled with sound deductive reasoning, will eventually whisper back, that what we are inquiring about is obviously some intangible, yet seemingly created thing, and such a powerful and ethereal type emergence as this evil surely is, it could only have originated from an even more powerful… indeed, totally omniscient and omnipotent Creative force.

Fortunately for us, this magnificently divine Entity came with a Manual, when if referred to, pretty clearly explains that this is indeed the source as well as the case for the origin of evil, and by studying ancient scripture, and discerning what they mean for our reality and temporal existence, we can arrive at a clearer understanding of why evil has been woven into the whole of humanity since the Garden of Eden.

First of all, evil is not a tangible thing. It is a manifesting, multi-faceted, cerebral process, which is unceasingly meted out with exacting purpose, yet always subject to termination at any point that the Creator chooses to end its existence and free humanity from its cruel vice-like grip. To get a child-like layman’s grasp on the reason for evil upon this earth, try thinking of it as a life sentence for all of us, in a federal prison that encompasses the entire planet, and you will begin to have a reasonable picture of what is really happening here. We are all guilty by association of the first sin, and evil is the iron bars of the holding cell that surrounds us, with thorns growing up from the floor.

Our sufferings on this earth, are both permissible and inescapable. They are the unrelenting judgment that was passed upon man from the time of Adam and Eve’s disobedience. It is utter foolishness to ask the atheist’s famous question, “If God exists, why does He allow bad things to happen?” They are supposed to happen because this temporal existence is a life sentence in the prison library, wherein we are supposed to be studying to get our diploma in General Studies 101, and through faith, an eventual pardon. We are all living in a fallen state, abounding with evil, and it is not meant to be a joy ride, totally free of consequences. We were born into sin and suffering, and we will die with it stuck to the bottom of our walking shoes.

The initial, manifestation of God’s awareness of evil, was the endowing of an abundance of pride, combined with free will like that of humans, in His creation of the most beautiful of all the angels. There are no detailed physical attributes recorded in the bible of this being, but he certainly was not red with pointed ears, horns, and a forked tail, and by logical association of him being synonymous with music, it is also doubtful he is a towering, snake-eyed, hulk-muscled beast. No, this lovable, pretty boy Robert Redford doppelganger, He singled out, and named Lucifer, or as he became affectionately known, ‘The Bright (helel) Morning Star’. He was in turn, given a distinguished position of authority as Heaven’s tremendously gifted choir director.

The ancient written records strongly imply, he is a master music composer and a superior orator, not a fighting angel like Gabriel or Michael. He has the gift of mental prowess and cunning manipulation, and once his pride over these attributes set in, and he began aspiring to the same status as God, God expelled him just as He knew He would be doing, along with all his faithful followers, who roughly totaled one-third of Heaven, and who we now refer to as demons, straight down here, of all the places in the universe, to our tiny earth, thus placing the epitome of evil on this very planet, for untold eons before creating us.

Of ‘Helel’ the bright one who stood behind the King of Tyre.

12 ‘Thus says the Lord GOD, “You were the seal of perfection, full of wisdom and perfect in beauty. 13 You were in Eden, the garden of God; every precious stone adorned you… Your settings and mountings were made of gold; on the day you were created they were prepared. 14 You were anointed as a guardian cherub, for so I ordained you. You were on the holy mount of God; you walked among the fiery stones. 15 You were blameless in your ways from the day you were created till wickedness was found in you.
Ezekiel 28:12-15

12 How you have fallen from heaven, morning star, son of the dawn! You have been cast down to the earth, you who once laid low the nations! 13 You said in your heart, “I will ascend to the heavens; I will raise my throne above the stars of God; I will sit enthroned on the mount of assembly, on the utmost heights of Mount Zaphon. I will ascend above the tops of the clouds; I will make myself like the Most High.”
Isaiah 14:12-14

Whether it was Lucifer himself or perhaps a comrade even more menacing than him, that appeared as a serpent-like entity in the tree of the fruit of knowledge of good and evil (come on, seriously… an apple?), growing in the garden of Eden, the fact remains, that they were already waiting in the shadows for homosapien’s arrival, and God knew that all too well. It cannot be denied, because He is the one setting everything in motion, from the point where He says, “Let there be light!”

Either we say God is in control, or we say He is not. The truth is, He was certainly powerful enough to have just as easily sent Lucifer and his horde all the way out to Pluto or another Galaxy altogether, but instead He purposely put us both together on the same rock. So why did the fallen angels need to be on this planet only to interferingly cohabit with us? Well, that becomes pretty obvious at this point. They are here to serve His purpose as an intrinsic and necessary half of the yinyang free will concept given specifically to homosapien. Are we to suppose that the omniscient Creator had no clue what Lucifer would do right from man’s start? If you think He was in the dark about it, I am afraid you have the wrong, and not so all knowing god.


Grandpa’s Wallet

In order to implant evil in man’s thoughts, all God had to do was place a single element in his path, which in this case was a unique tree in the garden, whos intoxicating fruit, when eaten, brings the yin and yang together, and opens the mind to corruption, like the lid on Pandora’s box,

This is uncannily similar to the old story of the grandfather placing his wallet on the table in front of his five-year-old grandchild and saying, “I have to leave the room for a minute, but I’ll be right back, so don’t you dare touch this wallet!” No sooner does he get out of sight, and peek around the corner, than the child has completely dragged everything in the wallet out, and onto the floor. Had God not purposely executed this very same scenario whereby man inevitably falls, and then is forced to seek God out, He would have just ended up with more angels, who were weaker than the original ones, that already knew Him. The entire human project would have been analogous to a soft, half-made clay jar being spun on the potter’s wheel, that suddenly goes off kilter and collapses back into a distorted heap of grey mud.

The Origin of Evil

Nothing exists that was not wrought by God, and unrelenting cogitative evil exists and resides in the minds of Satan and man.

“You are worthy, our Lord and God, to receive glory and honor and power, for you created all things, and by your will they were created and have their being.”
Revelation 4:11


As stated earlier, evil is a concept in the mind, and it is a concept that was first in God’s mind, not a tangible thing related to the laws of physics. You cannot see, touch, feel, smell or hear evil. It is not one of the fundamental forces of nature, nor does it consist of matter, energy, or the spatial dimensions of the universe, and it continues until terminated. Yet evil does reside. It takes up residence in the minds of both humans and fallen angels.

It is an unseen and extremely powerful force, which plays a pivotal role in bringing souls to a position of having to seek God for solace, and its consequence also includes a prolonged, agonizing stay of execution for Lucifer and his fallen company. This is understandably making them all the more vengeful to the bitter end. These angels were all created in the very presence of God, and because of this, there are none in need of discovering Him, nor are they created with the unique creative thinking ability we have been specially endowed with, and that God was needing, to ultimately commune with Him on His own personal level. In all of this, we are above the angels, and it is written, they serve us. Basically, we are the one-of-a-kind product of the Creator’s words, “Let us make man, in our own image”, not the image of angels, and definitely not the same mental capacity. God knows that pain and suffering make us who we are. It is just as the fictional Star Trek character, Captain Kirk said,

“Damn it, Bones, you’re a doctor. You know that pain and guilt can’t be taken away with a wave of a magic wand. They’re the things we carry with us, the things that make us who we are. If we lose them, we lose ourselves. I don’t want my pain taken away. I need my pain.”

God actually proclaims He is the original holder of the concept of evil, and there are several revealing passages within the Old Testament, which Christians try hard to avoid or scratch their heads in confusion, and those who do give them attention, immediately feel the need to explain it away, for the simple reason that they cannot fathom a benevolent Creator, being the author of such a seemingly negative concept. Being the conceptual author and being the perpetrator thereof, is two entirely different things.

I form the light, and create darkness; I make peace, and create evil; I, the Lord, do all these things.
Isaiah 45:7

Out of the mouth of the Most High proceedeth not evil and good?
Lamentations 3:38

Shall a trumpet be blown in the city, and the people not be afraid? Shall there be evil in a city, and the Lord hath not done it?
Amos 3:6

These are God’s words through His ancient prophets, so arguing it should prove easy since they are dust. Evil exists because God saw the necessity to take it from awareness to implementation, regardless of the inadequacy of human comprehension. Evil didn’t just walk around the corner of the garage one day, and say, “Hey, has anybody seen Lucifer around here lately?” In juxtaposition to God’s ability to go from drawing board to structure with His voice, Lucifer is powerless to create anything. His only expertise is manipulation and that, like his music, is nothing more than variations on a theme.

“All things came into being through Him, and apart from Him nothing came into being that has come into being.”
John 1:3

Evil went from concept to practice long before we got here, so it appears to me, you have to ask yourself this question. “Am I going to accept this above scribbling by the apostle John as truth, or rip out this part because it is utterly ridiculous and unacceptable.

“Well are you punk?”

 

Evil Truly Exists

Yes, but not without true purpose. Think about the definition of the word omniscience. Do we suppose that God, in His omniscience, was ever clueless that Lucifer would wail against Him, thus manifesting what was previously only an awareness in His mind? It is the element of evil that ultimately causes us to seek His face, whereas with angels who know Him, there is no positive benefit to it whatsoever. God didn’t want more angels. What He has always wanted is family that can attain closer to his level of understanding, and share creative thinking with Him, and subsequently, genuine love on a personal level. We were specially created with the extra capacity to achieve total sentience. Angels are clearly not capable of this, or we simply would not be here, with them written to be watching over us.

Apostle John, the Revelator wrote that one day in a far distant future, God plans to free Lucifer from his chains to once again roam helter-skelter, up and down, and to and fro in the earth, after Christ has reigned on earth for a peaceful one thousand years, which translates to intent to use evil one more time.

“And when the thousand years are expired, Satan shall be loosed out of his prison…”
Revelation 20:7

Only after that shall God finally return evil to a mere concept in His mind. It is doubtless unwise to argue the point of evil with God. It is His favorite Craftsman multi-purpose tool for bringing man to his knees, and without it, there is no hope of a higher attainment. I suggest you pull yourself up by your bootstraps, put your hard hat on and go with it.

By Douglas L. Duncan

Further Reading: A Good Reason for Evil.

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Endosymbiont Hypothesis and the Ironic Case for a Creator

endosymbionthypothesisandtheironic

BY FAZALE RANA – DECEMBER 12, 2018

i ·ro ·ny

The use of words to express something different from and often opposite to their literal meaning.
Incongruity between what might be expected and what actually occurs.

—The Free Dictionary

People often use irony in humor, rhetoric, and literature, but few would think it has a place in science. But wryly, this has become the case. Recent work in synthetic biology has created a real sense of irony among the scientific community—particularly for those who view life’s origin and design from an evolutionary framework.

Increasingly, life scientists are turning to synthetic biology to help them understand how life could have originated and evolved. But, they have achieved the opposite of what they intended. Instead of developing insights into key evolutionary transitions in life’s history, they have, ironically, demonstrated the central role intelligent agency must play in any scientific explanation for the origin, design, and history of life.

This paradoxical situation is nicely illustrated by recent work undertaken by researchers from Scripps Research (La Jolla, CA). Through genetic engineering, the scientific investigators created a non-natural version of the bacterium E. coli. This microbe is designed to take up permanent residence in yeast cells. (Cells that take up permanent residence within other cells are referred to as endosymbionts.) They hope that by studying these genetically engineered endosymbionts, they can gain a better understanding of how the first eukaryotic cells evolved. Along the way, they hope to find added support for the endosymbiont hypothesis.1

The Endosymbiont Hypothesis

Most biologists believe that the endosymbiont hypothesis (symbiogenesis) best explains one of the key transitions in life’s history; namely, the origin of complex cells from bacteria and archaea. Building on the ideas of Russian botanist Konstantin Mereschkowski, Lynn Margulis(1938–2011) advanced the endosymbiont hypothesis in the 1960s to explain the origin of eukaryotic cells.

Margulis’s work has become an integral part of the evolutionary paradigm. Many life scientists find the evidence for this idea compelling and consequently view it as providing broad support for an evolutionary explanation for the history and design of life.

According to this hypothesis, complex cells originated when symbiotic relationships formed among single-celled microbes after free-living bacterial and/or archaeal cells were engulfed by a “host” microbe. Presumably, organelles such as mitochondria were once endosymbionts. Evolutionary biologists believe that once engulfed by the host cell, the endosymbionts took up permanent residency, with the endosymbiont growing and dividing inside the host.

Over time, the endosymbionts and the host became mutually interdependent. Endosymbionts provided a metabolic benefit for the host cell—such as an added source of ATP—while the host cell provided nutrients to the endosymbionts. Presumably, the endosymbionts gradually evolved into organelles through a process referred to as genome reduction. This reduction resulted when genes from the endosymbionts’ genomes were transferred into the genome of the host organism.

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Figure 1: Endosymbiont hypothesis. Image credit: Wikipedia.

Life scientists point to a number of similarities between mitochondria and alphaproteobacteria as evidence for the endosymbiont hypothesis. (For a description of the evidence, see the articles listed in the Resources section.) Nevertheless, they don’t understand how symbiogenesis actually occurred. To gain this insight, scientists from Scripps Research sought to experimentally replicate the earliest stages of mitochondrial evolution by engineering E. coli and brewer’s yeast (S. cerevisiae) to yield an endosymbiotic relationship.

Engineering Endosymbiosis

First, the research team generated a strain of E. coli that no longer has the capacity to produce the essential cofactor thiamin. They achieved this by disabling one of the genes involved in the biosynthesis of the compound. Without this metabolic capacity, this strain becomes dependent on an exogenous source of thiamin in order to survive. (Because the E. coli genome encodes for a transporter protein that can pump thiamin into the cell from the exterior environment, it can grow if an external supply of thiamin is available.) When incorporated into yeast cells, the thiamin in the yeast cytoplasm becomes the source of the exogenous thiamin, rendering E. coli dependent on the yeast cell’s metabolic processes.

Next, they transferred the gene that encodes a protein called ADP/ATP translocase into the E. coli strain. This gene was harbored on a plasmid (which is a small circular piece of DNA). Normally, the gene is found in the genome of an endosymbiotic bacterium that infects amoeba. This protein pumps ATP from the interior of the bacterial cell to the exterior environment.2

The team then exposed yeast cells (that were deficient in ATP production) to polyethylene glycol, which creates a passageway for E. coli cells to make their way into the yeast cells. In doing so, E. coli becomes established as endosymbionts within the yeast cells’ interior, with the E. coli providing ATP to the yeast cell and the yeast cell providing thiamin to the bacterial cell.

Researchers discovered that once taken up by the yeast cells, the E. coli did not persist inside the cell’s interior. They reasoned that the bacterial cells were being destroyed by the lysosomal degradation pathway. To prevent their destruction, the research team had to introduce three additional genes into the E. coli from three separate endosymbiotic bacteria. Each of these genes encodes proteins—called SNARE-like proteins—that interfere with the lysosomal destruction pathway.

Finally, to establish a mutualistic relationship between the genetically-engineered strain of E. coli and the yeast cell, the researchers used a yeast strain with defective mitochondria. This defect prevented the yeast cells from producing an adequate supply of ATP. Because of this limitation, the yeast cells grow slowly and would benefit from the E. coli endosymbionts, with the engineered capacity to transport ATP from their cellular interior to the exterior environment (the yeast cytoplasm.)

The researchers observed that the yeast cells with E. coli endosymbionts appeared to be stable for 40 rounds of cell doublings. To demonstrate the potential utility of this system to study symbiogenesis, the research team then began the process of genome reduction for the E. coli endosymbionts. They successively eliminated the capacity of the bacterial endosymbiont to make the key metabolic intermediate NAD and the amino acid serine. These triply-deficient E. coli strains survived in the yeast cells by taking up these nutrients from the yeast cytoplasm.

Evolution or Intentional Design?

The Scripps Research scientific team’s work is impressive, exemplifying science at its very best. They hope that their landmark accomplishment will lead to a better understanding of how eukaryotic cells appeared on Earth by providing the research community with a model system that allows them to probe the process of symbiogenesis. It will also allow them to test the various facets of the endosymbiont hypothesis.

In fact, I would argue that this study already has made important strides in explaining the genesis of eukaryotic cells. But ironically, instead of proffering support for an evolutionary origin of eukaryotic cells (even though the investigators operated within the confines of the evolutionary paradigm), their work points to the necessary role intelligent agency must have played in one of the most important events in life’s history.

This research was executed by some of the best minds in the world, who relied on a detailed and comprehensive understanding of biochemical and cellular systems. Such knowledge took a couple of centuries to accumulate. Furthermore, establishing mutualistic interactions between the two organisms required a significant amount of ingenuity—genius that is reflected in the experimental strategy and design of their study. And even at that point, execution of their experimental protocols necessitated the use of sophisticated laboratory techniques carried out under highly controlled, carefully orchestrated conditions. To sum it up: intelligent agency was required to establish the endosymbiotic relationship between the two microbes.

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Figure 2: Lab researcher. Image credit: Shutterstock.

Or, to put it differently, the endosymbiotic relationship between these two organisms was intelligently designed. (All this work was necessary to recapitulate only the presumed first step in the process of symbiogenesis.) This conclusion gains added support given some of the significant problems confronting the endosymbiotic hypothesis. (For more details, see the Resources section.) By analogy, it seems reasonable to conclude that eukaryotic cells, too, must reflect the handiwork of a Divine Mind—a Creator.

Resources

Endnotes

  1. Angad P. Mehta et al., “Engineering Yeast Endosymbionts as a Step toward the Evolution of Mitochondria,” Proceedings of the National Academy of Sciences, USA 115 (November 13, 2018): doi:10.1073/pnas.1813143115.
  2. ATP is a biochemical that stores energy used to power the cell’s operation. Produced by mitochondria, ATP is one of the end products of energy harvesting pathways in the cell. The ATP produced in mitochondria is pumped into the cell’s cytoplasm from within the interior of this organelle by an ADP/ATP transporter.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/12/12/endosymbiont-hypothesis-and-the-ironic-case-for-a-creator

Did Neanderthals Start Fires?

neanderthalsstartfire

BY FAZALE RANA – DECEMBER 5, 2018

It is one of the most iconic Christmas songs of all time.

Written by Bob Wells and Mel Torme in the summer of 1945, “The Christmas Song” (subtitled “Chestnuts Roasting on an Open Fire”) was crafted in less than an hour. As the story goes, Wells and Torme were trying to stay cool during the blistering summer heat by thinking cool thoughts and then jotting them down on paper. And, in the process, “The Christmas Song” was born.

Many of the song’s lyrics evoke images of winter, particularly around Christmastime. But none has come to exemplify the quiet peace of a Christmas evening more than the song’s first line, “Chestnuts roasting on an open fire . . . ”

Gathering around the fire to stay warm, to cook food, and to share in a community has been an integral part of the human experience throughout history—including human prehistory. Most certainly our ability to master fire played a role in our survival as a species and in our ability as human beings to occupy and thrive in some of the world’s coldest, harshest climates.

But fire use is not limited only to modern humans. There is strong evidence that Neanderthals made use of fire. But, did these creatures have control over fire in the same way we do? In other words, did Neanderthals master fire? Or, did they merely make opportunistic use of natural fires? These questions are hotly debated by anthropologists today and they contribute to a broader discussion about the cognitive capacity of Neanderthals. Part of that discussion includes whether these creatures were cognitively inferior to us or whether they were our intellectual equals.

In an attempt to answer these questions, a team of researchers from the Netherlands and France characterized the microwear patterns on bifacial (having opposite sides that have been worked on to form an edge) tools made from flint recovered from Neanderthal sites, and concluded that the wear patterns suggest that these hominins used pyrite to repeatedly strike the flint. This process generates sparks that can be used to start fires.1 To put it another way, the researchers concluded that Neanderthals had mastery over fire because they knew how to start fires.

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Figure 1: Biface tools for cutting or scraping. Image credit: Shutterstock

However, a closer examination of the evidence along with results of other studies, including recent insight into the cause of Neanderthal extinction, raises significant doubts about this conclusion.

What Do the Microwear Patterns on Flint Say?

The investigators focused on the microwear patterns of flint bifaces recovered from Neanderthal sites as a marker for fire mastery because of the well-known practice among hunter-gatherers and pastoralists of striking flint with pyrite (an iron disulfide mineral) to generate sparks to start fires. Presumably, the first modern humans also used this technique to start fires.

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Figure 2: Starting a fire with pyrite and flint. Image credit: Shutterstock

The research team reasoned that if Neanderthals started fires, they would use a similar tactic. Careful examination of the microwear patterns on the bifaces led the research team to conclude that these tools were repeatedly struck by hard materials, with the strikes all occurring in the same direction along the bifaces’ long axis.

The researchers then tried to experimentally recreate the microwear pattern in a laboratory setting. To do so, they struck biface replicas with a number of different types of materials, including pyrites, and concluded that the patterns produced by the pyrite strikes most closely matched the patterns on the bifaces recovered from Neanderthal sites. On this basis, the researchers claim that they have found evidence that Neanderthals deliberately started fires.

Did Neanderthals Master Fire?

While this conclusion is possible, at best this study provides circumstantial, not direct, evidence for Neanderthal mastery of fire. In fact, other evidence counts against this conclusion. For example, bifaces with the same type of microwear patterns have been found at other Neanderthal sites, locales that show no evidence of fire use. These bifaces would have had a range of usages, including butchery of the remains of dead animals. So, it is possible that these tools were never used to start fires—even at sites with evidence for fire usage.

Another challenge to the conclusion comes from the failure to detect any pyrite on the bifaces recovered from the Neanderthal sites. Flint recovered from modern human sites shows visible evidence of pyrite. And yet the research team failed to detect even trace amounts of pyrite on the Neanderthal bifaces during the course of their microanalysis.

This observation raises further doubt about whether the flint from the Neanderthal sites was used as a fire starter tool. Rather, it points to the possibility that Neanderthals struck the bifaces with materials other than pyrite for reasons not yet understood.

The conclusion that Neanderthals mastered fire also does not square with results from other studies. For example, a careful assessment of archaeological sites in southern France occupied by Neanderthals from about 100,000 to 40,000 years ago indicates that Neanderthals could not create fire. Instead, these hominins made opportunistic use of natural fire when it was available to them.2

These French sites do show clear evidence of Neanderthal fire use, but when researchers correlated the archaeological layers displaying evidence for fire use with the paleoclimate data, they found an unexpected pattern. Neanderthals used fire during warm climate conditions and failed to use fire during cold periods—the opposite of what would be predicted if Neanderthals had mastered fire.

Lightning strikes that would generate natural fires are much more likely to occur during warm periods. Instead of creating fire, Neanderthals most likely harnessed natural fire and cultivated it as long as they could before it extinguished.

Another study also raises questions about the ability of Neanderthals to start fires.3 This research indicates that cold climates triggered Neanderthal extinctions. By studying the chemical composition of stalagmites in two Romanian caves, an international research team concluded that there were two prolonged and extremely cold periods between 44,000 and 40,000 years ago. (The chemical composition of stalagmites varies with temperature.)

The researchers also noted that during these cold periods, the archaeological record for Neanderthals disappears. They interpret this disappearance to reflect a dramatic reduction in Neanderthal population numbers. Researchers speculate that when this population downturn took place during the first cold period, modern humans made their way into Europe. Being better suited for survival in the cold climate, modern human numbers increased. When the cold climate mitigated, Neanderthals were unable to recover their numbers because of the growing populations of modern humans in Europe. Presumably, after the second cold period, Neanderthal numbers dropped to the point that they couldn’t recover, and hence, became extinct.

But why would modern humans be more capable than Neanderthals of surviving under extremely cold conditions? It seems as if it should be the other way around. Neanderthals had a hyper-polar body design that made them ideally suited to withstand cold conditions. Neanderthal bodies were stout and compact, comprised of barrel-shaped torsos and shorter limbs, which helped them retain body heat. Their noses were long and sinus cavities extensive, which helped them warm the cold air they breathed before it reached their lungs. But, despite this advantage, Neanderthals died out and modern humans thrived.

Some anthropologists believe that the survival discrepancy could be due to dietary differences. Some data indicates that modern humans had a more varied diet than Neanderthals. Presumably, these creatures primarily consumed large herbivores—animals that disappeared when the climatic conditions turned cold, thereby threatening Neanderthal survival. On the other hand, modern humans were able to adjust to the cold conditions by shifting their diets.

But could there be a different explanation? Could it be that with their mastery of fire, modern humans were able to survive cold conditions? And did Neanderthals die out because they could not start fires?

Taken in its entirety, the data seems to indicate that Neanderthals lacked mastery of fire but could use it opportunistically. And, in a broader context, the data indicates that Neanderthals were cognitively inferior to humans.

What Difference Does It Make?

One of the most important ideas taught in Scripture is that human beings uniquely bear God’s image. As such, every human being has immeasurable worth and value. And because we bear God’s image, we can enter into a relationship with our Maker.

However, if Neanderthals possessed advanced cognitive ability just like that of modern humans, then it becomes difficult to maintain the view that modern humans are unique and exceptional. If human beings aren’t exceptional, then it becomes a challenge to defend the idea that human beings are made in God’s image.

Yet, claims that Neanderthals are cognitive equals to modern humans fail to withstand scientific scrutiny, time and time, again. Now it’s time to light a fire in my fireplace and enjoy a few contemplative moments thinking about the real meaning of Christmas.

Resources

Endnotes

  1. A. C. Sorensen, E. Claud, and M. Soressi, “Neanderthal Fire-Making Technology Inferred from Microwear Analysis,” Scientific Reports 8 (July 19, 2018): 10065, doi:10.1038/s41598-018-28342-9.
  2. Dennis M. Sandgathe et al., “Timing of the Appearance of Habitual Fire Use,” Proceedings of the National Academy of Sciences, USA 108 (July 19, 2011), E298, doi:10.1073/pnas.1106759108; Paul Goldberg et al., “New Evidence on Neandertal Use of Fire: Examples from Roc de Marsal and Pech de l’Azé IV,” Quaternary International 247 (2012): 325–40, doi:10.1016/j.quaint.2010.11.015; Dennis M. Sandgathe et al., “On the Role of Fire in Neandertal Adaptations in Western Europe: Evidence from Pech de l’Azé IV and Roc de Marsal, France,” PaleoAnthropology (2011): 216–42, doi:10.4207/PA.2011.ART54.
  3. Michael Staubwasser et al., “Impact of Climate Change on the Transition of Neanderthals to Modern Humans in Europe,” Proceedings of the National Academy of Sciences, USA 115 (September 11, 2018): 9116–21, doi:10.1073/pnas.1808647115.

Rembrandt’s fingerprints spotted in 400-year-old painting

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The Dutch master is thought to have touched the oil paint on Study Of A Head Of A Young Man when it was still wet.

By Stephen White
21:21, 21 Nov. 2018

Study Of A Head Of A Young Man portrays Rembrandt’s model as Jesus (Image: PA)
Fingerprints thought to be those of Dutch master Rembrandt have been discovered in a small oil sketch almost 400 years old.

Study Of A Head Of A Young Man, measuring just 10in high, is expected to fetch about £6million when it is auctioned in London next month.

Buried in the original layer of paint, in the lower edge of the “powerful and touching” 17th century portrait, experts found what are believed to be the Dutch master’s thumbprints.

No other prints by the painter, said to be the “foremost master of the Western artistic tradition”, have ever been found.

While it is impossible to confirm the prints are those of Rembrandt, who is famous for his portraits and use of light and shadow, experts believe they are the “only known fingerprints of the Dutch master”.

They were uncovered during a process of technical examination and restoration, which included pigment analyses, X-ray and infra-red imaging, just before the painting went on display in the US and the Louvre, in Paris.

George Gordon, worldwide co-chairman of Sotheby’s Old Master paintings, who are auctioning the work, called the find an “extraordinary discovery”.

The fingerprints were left on the 1655 painting when the paint was still wet.

The Next Rembrandt: Dutch Master ‘brought back to life’ for one last painting
“You often get finger and thumbprints in the varnish of painting, but that doesn’t really tell you anything of interest,” he said. “This is in the original paint.

“This shows that Rembrandt was happy with the painting while it was still wet. He painted it very quickly.

“But what is certain is that it is somebody that picked up the painting as soon as it was finished.”

He added: “While as far as we know no comparable finger or thumbprints of Rembrandt have been found in other works to confirm the conclusion, the discovery of the marks in the original layer of paint…. make their connection to the artist highly credible.”

He said that the portrait, dating from around 1655, has a “spiritual and emotional impact”.

“We know he worked really quickly and you can also see and feel it in this painting,” he said.

“When Rembrandt applies thick layers of paint, some of the colour leaches through. It has an intense visceral quality and is astonishingly well preserved.”

He added: “I suspect people will now look for fingerprints in other paintings.”

Michel van de Laar, a conservator in Amsterdam who helped lead the research, said: “The work was also determined to have been executed in one sitting.

“The discovery of the fingerprints is further testament to the speed with which the work was likely executed and provides fresh insight into Rembrandt’s complex but swift painting technique.”

Study Of A Head Of A Young Man portrays Rembrandt’s model as Jesus, with his hands clasped in prayer, and has been praised for the artist’s ability to “render human emotions”.

Spider Silk Inspires New Technology and the Case for a Creator

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BY FAZALE RANA – NOVEMBER 28, 2018
Mark your calendars!

On December 14th (2018), Columbia Pictures—in collaboration with Sony Pictures Animation—will release a full-length animated feature: Spider-Man: Into the Spider-Verse. The story features Miles Morales, an Afro-Latino teenager, as Spider-Man.

Morales accidentally becomes transported from his universe to ours, where Peter Parker is Spider-Man. Parker meets Morales and teaches him how to be Spider-Man. Along the way, they encounter different versions of Spider-Man from alternate dimensions. All of them team up to save the multiverse and to find a way to return back to their own versions of reality.

What could be better than that?

In 1962, Spider-Man’s creators, Stan Lee and Steve Ditko, drew inspiration for their superhero in the amazing abilities of spiders. And today, engineers find similar inspiration, particularly, when it comes to spider silk. The remarkable properties of spider’s silk is leading to the creation of new technologies.

Synthetic Spider Silk

Engineers are fascinated by spider silk because this material displays astonishingly high tensile strength and ductility (pliability), properties that allow it to absorb huge amounts of energy before breaking. Only one-sixth the density of steel, spider silk can be up to four times stronger, on a per weight basis.

By studying this remarkable substance, engineers hope that they can gain insight and inspiration to engineer next-generation materials. According to Northwestern University researcher Nathan C. Gianneschi, who is attempting to produce synthetic versions of spider silk, “One cannot overstate the potential impact on materials and engineering if we can synthetically replicate the natural process to produce artificial fibers at scale. Simply put, it would be transformative.”1

Gregory P. Holland of San Diego State University, one of Gianneschi’s collaborators, states, “The practical applications for materials like this are essentially limitless.”2 As a case in point, synthetic versions of spider silk could be used to make textiles for military personnel and first responders and to make construction materials such as cables. They would also have biomedical utility and could be used to produce environmentally friendly plastics.

The Quest to Create Synthetic Spider Silk

But things aren’t that simple. Even though life scientists and engineers understand the chemical structure of spider’s silk and how its structural features influence its mechanical properties, they have not been able to create synthetic versions of it with the same set of desired properties.

 

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Figure 1: The Molecular Architecture of Spider Silk. Fibers of spider silk consist of proteins that contain crystalline regions separated by amorphous regions. The crystals form from regions of the protein chain that fold into structures called beta-sheets. These beta-sheets stack together to give the spider silk its tensile strength. The amorphous regions give the silk fibers ductility. Image credit: Chen-Pan Liao.

Researchers working to create synthetic spider silk speculate that the process by which the spider spins the silk may play a critical role in establishing the biomaterial’s tensile strength and ductility. Before it is extruded, silk exists in a precursor form in the silk gland. Researchers think that the key to generating synthetic spider silk with the same properties as naturally formed spider silk may be found by mimicking the structure of the silk proteins in precursor form.

Previous work suggests that the proteins that make up spider silk exist as simple micelles in the silk gland and that when spun from this form, fibers with greater-than-steel strength are formed. But researchers’ attempts to apply this insight in a laboratory setting failed to yield synthetic silk with the desired properties.

The Structure of Spider Silk Precursors

Hoping to help unravel this problem, a team of American collaborators led by Gianneschi and Holland recently provided a detailed characterization of the structure of the silk protein precursors in spider glands.3 They discovered that the silk proteins form micelles, but the micelles aren’t simple. Instead, they assemble into a complex structure comprised of a hierarchy of subdomains. Researchers also learned that when they sheared these nanoassemblies of precursor proteins, fibers formed. If they can replicate these hierarchical nanostructures in the lab, researchers believe they may be able to construct synthetic spider silk with the long-sought-after tensile strength and ductility.

Biomimetics and Bioinspiration

Attempts to find inspiration for new technology is n0t limited to spider silk. It has become rather commonplace for engineers to employ insights from arthropod biology (which includes spiders and insects) to solve engineering problems and to inspire the invention of new technologies—even technologies unlike anything found in nature. In fact, I discuss this practice in an essay I contributed for the book God and the World of Insects.

This activity falls under the domain of two relatively new and exciting areas of engineering known as biomimetics and bioinspiration. As the names imply, biomimetics involves direct mimicry of designs from biology, whereas bioinspiration relies on insights from biology to guide the engineering enterprise.

The Converse Watchmaker Argument for God’s Existence

The idea that biological designs can inspire engineering and technology advances is highly provocative. It highlights the elegant designs found throughout the living realm. In the case of spider silk, design elegance is not limited to the structure of spider silk but extends to its manufacturing process as well—one that still can’t be duplicated by engineers.

The elegance of these designs makes possible a new argument for God’s existence—one I have named the converse Watchmaker argument. (For a detailed discussion see the essay I contributed to the book Building Bridges, entitled, “The Inspirational Design of DNA.”)

The argument can be stated like this: if biological designs are the work of a Creator, then these systems should be so well-designed that they can serve as engineering models for inspiring the development of new technologies. Indeed, this scenario is what scientists observe in nature. Therefore, it becomes reasonable to think that biological designs are the work of a Creator.

Biomimetics and the Challenge to the Evolutionary Paradigm

From my perspective, the use of biological designs to guide engineering efforts seems fundamentally at odds with evolutionary theory. Generally speaking, evolutionary biologists view biological systems as the products of an unguided, historically contingent process that co-opts preexisting systems to cobble together new ones. Evolutionary mechanisms can optimize these systems, but even then they are, in essence, still kludges.

Given the unguided nature of evolutionary mechanisms, does it make sense for engineers to rely on biological systems to solve problems and inspire new technologies? Is it in alignment with evolutionary beliefs to build an entire subdiscipline of engineering upon mimicking biological designs? I would argue that these engineering subdisciplines do not fit with the evolutionary paradigm.

On the other hand, biomimetics and bioinspiration naturally flow out of a creation model approach to biology. Using designs in nature to inspire engineering only makes sense if these designs arose from an intelligent Mind, whether in this universe or in any of the dimensions of the Spider-Verse.

Resources

Endnotes

  1. Northwestern University, “Mystery of How Black Widow Spiders Create Steel-Strength Silk Webs further Unravelled,” Phys.org, Science X, October 22, 2018, https://phys.org/news/2018-10-mystery-black-widow-spiders-steel-strength.html.
  2. Northwestern University, “Mystery of How Black Widow Spiders Create.”
  3. Lucas R. Parent et al., “Hierarchical Spidroin Micellar Nanoparticles as the Fundamental Precursors of Spider Silks,” Proceedings of the National Academy of Sciences USA (October 2018), doi:10.1073/pnas.1810203115.

The Smallest Thing There Is

The science of quantum physics, or the world of the very small.
By Douglas Duncan

Did you ever ask as a child, “What is the very smallest thing that there is?”, or “How small can something be before it becomes nothing?” Asking those two questions usually give rise to the grander third one, “What is the opposite of the universe?” Well, it is just a theory at this point, as there is currently no technological way of observing; but quantum physicists now theorize that the at the very bottom of the ladder, is nothing more than vibrating bits of oscillating waves, that for now, can only be described as ‘strings’. They conjecture two types… ‘open’ and ‘closed’ strings.

Traveling down through the world of the very small… smaller than the atom, smaller than protons or neutrons, smaller than electrons, still smaller than neutrinos and quarks, continuing downward beyond photons and gluons, we finally arrive at the point where ‘No man has gone before’.

There really is no way to explain String Theory, to most of us, but I researched and sought for the least technical article on the subject, and have included it below.

Just make an attempt to read through it, maybe twice, and you may (or may not) begin to see what the physicists are discussing.

I like the guitar string analogy best, as I would say that most people have observed how a plucked guitar string appears to look like a bunch of strings as it’s vibrating. By the way, cats go crazy when you pluck a string in front of them because they see every one of those vibrations as a single string.

I found the following article on string theory to be extremely enlightening and it is written with a more fundamental and easier to understand explanation. Even so, you still have to concentrate some (or at least browse what makes sense), but it will serve as an excellent beginners guide, and you will be able to discuss and learn further about our quantum universe from gaining a handle on it here.


Article:
Think of a guitar string that has been tuned by stretching the string under tension across the guitar. Depending on how the string is plucked and how much tension is in the string, different musical notes will be created by the string. These musical notes could be said to be excitation modes of that guitar string under tension.

In a similar manner, in string theory, the elementary particles we observe in particle accelerators could be thought of as the “musical notes” or excitation modes of elementary strings.

In string theory, as in guitar playing, the string must be stretched under tension in order to become excited. However, the strings in string theory are floating in space-time; they aren’t tied down to a guitar. Nonetheless, they have tension. The string tension in string theory is denoted by the quantity 1/(2 p a’), where a’ is pronounced “alpha prime” and is equal to the square of the string length scale.

If string theory is to be a theory of quantum gravity, then the average size of a string should be somewhere near the length scale of quantum gravity, called the Planck length, which is about 10-33 centimeters, or about a millionth of a billionth of a billionth of a billionth of a centimeter. Unfortunately, this means that strings are way too small to see by current or expected particle physics technology (or financing!!) and so string theorists must devise more clever methods to test the theory than just looking for little strings in particle experiments.

String theories are classified according to whether or not the strings are required to be closed loops, and whether or not the particle spectrum includes fermions. In order to include fermions in string theory, there must be a special kind of symmetry called supersymmetry, which means for every boson (particle that transmits a force) there is a corresponding fermion (particle that makes up matter). So supersymmetry relates the particles that transmit forces to the particles that make up matter.

Supersymmetric partners to currently known particles have not been observed in particle experiments, but theorists believe this is because supersymmetric particles are too massive to be detected at current accelerators. Particle accelerators could be on the verge of finding evidence for high energy supersymmetry in the next decade.

Evidence for supersymmetry at high energy would be compelling evidence that string theory was a good mathematical model for Nature at the smallest distance scales.


doubled

Vicissitudes from the Hollow

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By Douglas L. Duncan

Eleven years lived in eastern Kentucky.
Eleven long years where the sun flickers light.
Encompassed by mountains, that reach to the heavens.
Gazing up, thru a portal of stars in the night.

Where trash bags and milk jugs float down the Tug River,
and the coal smoke from chimneys add soot to the rain.
There’s no warmth in the hollows, no hope for the miner,
and the floods and the forest fires make known their claim.

Man’s not meant to live there, corn grows on the hillside,
and they gather the ears to the bins by the stills.
Then they turn it to whiskey, and give it to family,
who drink to forget all their troubles and ills.

I am blessed to have lived there, and I’ve learned a great lesson.
Never walk thru this life, with a longing for gold.
Be grateful for sunshine, be grateful for breakfast.
And remember the place, whence this story is told.


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Think Speak

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In George Orwell’s novel 1984, ‘Think-Speak’ is the name of a universal language of permissible word usage in a dismal dystopian future, whose purpose is to convey a structured monologue of the goings on of daily life, with the goal of having everyone be aligned on thought while eliminating all emotion during the course of communication.

My Definition of ‘Think Speak’, unlike Orwell’s, retains emotions and is the act of condensing a more complete, comprehensive thought process that one has just broken down (analyzed) into its constituent parts within their mind. This summary is stated as a quote, cliche or perhaps an abbreviated ‘short line’ they have just coined themselves.

For example, one has been thinking extensively about how they have spent their life’, or, they have just completed breaking down all the aspects of a particular issue or situation. All of a sudden, a ‘Think Speak’ pops into their head, so they summarily utter something peculiar such as “Life’s Been Good So Far”, or “You can never go back” (i.e. you burned the bridges), etc.

Again, when they realize that they have exhausted the issue, a remembered phrase or quote may come to mind that nicely ‘sums’ up everything that was just pondered over. For them, it is like giving the mental work a title.

While this ‘Think Speak’ summarizing makes perfect sense to the one who worked through the thought process, it is apt to sound or appear (if written) to another, as ambiguous or confusing. It might be construed as a parable or quote that doesn’t fit within the present conversation. It may indeed seem that the one doing the ‘Think Speak’ has simply lost their mind.

The caveat of ‘Think Speak’ is that the recipient simply can’t read the thinker’s mind, although the thinker falsely assumes that the recipient’s mind is one with theirs so it must be a ‘given’.

Footnote:
‘The result of using ‘Think Speak’ is somewhat analogous to the humorous, well worn defining of the word ‘Assume’. To Assume, can often times make an ‘Ass of You and Me’.


doubled